Package phase

Class PbwtIbsData

  • public class PbwtIbsData
extends java.lang.Object

    Class PbwtIbsData contains parameters and data for finding haplotypes that share an IBS segment with a target haplotype.

    • Constructor Summary

      Constructors 
      Constructor Description
      PbwtIbsData​(PhaseData phaseData, CodedSteps codedSteps)
      Constructs a new PbwtIbsData instance from the specified data.

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      CodedSteps codedSteps()
      Returns the coded steps.
      int maxBackoffSteps()
      Returns the number of backoff steps
      int nBatches()
      Returns the number of batches.
      int nCandidates()
      Returns the number of candidate haplotypes
      int nHaps()
      Returns the total number of target and reference haplotypes.
      int nOverlapSteps()
      Returns the number of overlap steps
      int nTargHaps()
      Returns the number of target haplotypes.
      int stepsPerBatch()
      Returns the number of steps per batch

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Constructor Detail

      • PbwtIbsData

        public PbwtIbsData​(PhaseData phaseData,
                   CodedSteps codedSteps)
        Constructs a new PbwtIbsData instance from the specified data.
        Parameters:
        phaseData - the current genotype phase estimates and parameter values
        codedSteps - the coded steps
        Throws:
        java.lang.IllegalArgumentException - if phaseData.fpd().stage1Steps() != codedSteps.steps()
        java.lang.IllegalArgumentException - if phaseData.fpd().stage1XRefGT()!=codedSteps.refHaps()
        java.lang.IllegalArgumentException - if phaseData.fpd().targGT().samples()!=codedSteps.targSamples()
        java.lang.NullPointerException - if phaseData == null || codedSteps == null

    • Method Detail

      • codedSteps

        public CodedSteps codedSteps()
        Returns the coded steps.
        Returns:
        the codedSteps

      • nHaps

        public int nHaps()
        Returns the total number of target and reference haplotypes.
        Returns:
        the total number of target and reference haplotypes

      • nTargHaps

        public int nTargHaps()
        Returns the number of target haplotypes.
        Returns:
        the number of target haplotypes

      • nCandidates

        public int nCandidates()
        Returns the number of candidate haplotypes
        Returns:
        the number of candidate haploytpes

      • nOverlapSteps

        public int nOverlapSteps()
        Returns the number of overlap steps
        Returns:
        the number of overlap steps

      • maxBackoffSteps

        public int maxBackoffSteps()
        Returns the number of backoff steps
        Returns:
        the number of backoff steps

      • stepsPerBatch

        public int stepsPerBatch()
        Returns the number of steps per batch
        Returns:
        the number of steps per batch

      • nBatches

        public int nBatches()
        Returns the number of batches.
        Returns:
        the number of batches